How reliable are these numbers? They’re probably in the right ballpark. Here are some things to keep in mind about them:

They usually come from very small samplesThis experiment, for example, estimates the mutation rate of one phage (specialized anti-bacteria virus) by:

Starting with a known number of phages and hosts

Putting the phages in a situation where it’ll be very obvious if they have a mutation that breaks a particular gene

Extracting the now-obvious mutants

Sequencing the broken gene in a bunch of mutants

Extrapolating the mutation rate in this one gene to the entire genome

They probably don’t catch all mutations
In the experiment above, they basically count the phages that can’t survive due to a particular genetic disease, and then sequence the part that broke. But if that same gene had a mutation that didn’t break it, the researchers would never know.

There are mutation hotspots and cold spots
As far as scientists know, some genes mutate much more than others. There are even certain codons – 3-letter codes for single amino acids inside proteins – that are extremely “hot”, while everything around them is not. They mutate so much more than most of the genome that they can throw off the average. For example, in E. coli’s LacI gene (whatever that is), ~72% of mutations to that gene happen in a string of 13 nucleotides (genetic letters).